I rescued a horse that was severly neglected and he had rainrot on his hindquarters and his back. It took several weeks, but we gave him medicated shampoo baths about 5x per week. After washing it and gently scrubbing off the rain rot (as much as he could tolerant it - the skin is obviously sensitive) we dried the areas really well and put baby powder on them. This worked very well. He was looking beautiful in about 3 weeks. It was the severest case of rain rot that my stable owner had ever seen, and she's been around horses for 60+ years.